Enzyme Site Finder

Objective of the Script: This tool is designed to identify restriction enzyme recognition sites within a provided IUPAC nucleotide pattern. By expanding the IUPAC pattern into all possible DNA sequences, the script matches these sequences against known restriction enzyme recognition sites. The tool highlights where enzyme sites fit within the original pattern, maintaining the integrity of IUPAC symbols outside the matched regions. This is particularly useful for researchers and genetic engineers looking to identify potential restriction sites within complex or degenerate DNA sequences.

How to Use the Tool:

1. Input Your IUPAC Pattern:

• Enter your nucleotide sequence using IUPAC notation in the provided input area.
• The pattern can include standard bases (A, C, G, T) and degenerate IUPAC symbols (e.g., N, R, Y).

2. Understanding the IUPAC Symbols:

• A: Adenine
• C: Cytosine
• G: Guanine
• T: Thymine
• N: Any base (A, C, G, T)
• R: Purine (A, G)
• Y: Pyrimidine (C, T)
• Additional symbols are also supported as per IUPAC standards.

3. Set Analysis Parameters:

• Review the list of restriction enzymes included in the tool.
• If desired, you can customize the enzyme list or add new enzymes by modifying the script.

4. Processing Your Pattern:

• Click the 'Analyze' button to start the process.
• The script will expand your IUPAC pattern into all possible sequences and compare each against the recognition sequences of the restriction enzymes.

5. Visualizing the Results:

• The tool will display a table with two columns:
  • Enzyme: The name of the restriction enzyme that matched.
  • Pattern with Highlighted Site: Your original IUPAC pattern with the matched restriction site highlighted in red for easy visualization.

6. Review and Interpret Results:

• Check the highlighted sequences to ensure they match your experimental needs.
• The tool preserves the original IUPAC notation outside the enzyme recognition site, allowing you to easily identify where the enzyme fits.

7. Customizing and Extending:

• You can modify the list of restriction enzymes in the script to suit specific needs or add new enzymes as required.
• For more complex analysis, consider integrating the script into a broader pipeline or using it in conjunction with other sequence analysis tools.

Note: This tool provides a flexible approach to identifying restriction enzyme sites within complex nucleotide patterns. It is designed for experimental and research purposes, and while it strives for accuracy, it is recommended to manually review results, especially for critical applications. The tool is part of an experimental framework and is used at your own risk.